python main.py Fig.5F_FA300-Y0844-Cortex_ABE_S115_L001_R1_001.fastq.gz out/Fig.5F_FA300-Y0844-Cortex_ABE_S115_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA300-Y0845-Cortex_ABE_S120_L001_R1_001.fastq.gz out/Fig.5F_FA300-Y0845-Cortex_ABE_S120_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA300-Y0850-Cortex_ABE_S125_L001_R1_001.fastq.gz out/Fig.5F_FA300-Y0850-Cortex_ABE_S125_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA300-Y0852-Cortex-ABE_S130_L001_R1_001.fastq.gz out/Fig.5F_FA300-Y0852-Cortex-ABE_S130_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA300-Y0853-Cortex_ABE_S135_L001_R1_001.fastq.gz out/Fig.5F_FA300-Y0853-Cortex_ABE_S135_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA300-Y0896-Untreated_S61_L001_R1_001.fastq.gz out/Fig.5F_FA300-Y0896-Untreated_S61_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA300-Y0896-Untreated_S62_L001_R1_001.fastq.gz out/Fig.5F_FA300-Y0896-Untreated_S62_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA300-Y0896-Untreated_S63_L001_R1_001.fastq.gz out/Fig.5F_FA300-Y0896-Untreated_S63_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA300-Y0896-Untreated_S64_L001_R1_001.fastq.gz out/Fig.5F_FA300-Y0896-Untreated_S64_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA800-Y0842-Cortex-ABE_S65_L001_R1_001.fastq.gz out/Fig.5F_FA800-Y0842-Cortex-ABE_S65_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA800-Y0846-Cortex-ABE_S69_L001_R1_001.fastq.gz out/Fig.5F_FA800-Y0846-Cortex-ABE_S69_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA800-Y0847-Cortex-ABE_S74_L001_R1_001.fastq.gz out/Fig.5F_FA800-Y0847-Cortex-ABE_S74_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA800-Y0848-Cortex-ABE_S79_L001_R1_001.fastq.gz out/Fig.5F_FA800-Y0848-Cortex-ABE_S79_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA800-Y0883-Untreated_S84_L001_R1_001.fastq.gz out/Fig.5F_FA800-Y0883-Untreated_S84_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA800-Y0883-Untreated_S86_L001_R1_001.fastq.gz out/Fig.5F_FA800-Y0883-Untreated_S86_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_FA800-Y0883-Untreated_S87_L001_R1_001.fastq.gz out/Fig.5F_FA800-Y0883-Untreated_S87_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_Y960-GAA800-CTX_ABE_S194_L001_R1_001.fastq.gz out/Fig.5F_Y960-GAA800-CTX_ABE_S194_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_Y1602_GAA800_Untreated_S176_L001_R1_001.fastq.gz out/Fig.5F_Y1602_GAA800_Untreated_S176_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_Y2383Ctx-ABE_S168_L001_R1_001.fastq.gz out/Fig.5F_Y2383Ctx-ABE_S168_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_Y2384Cortex_ABE_S182_L001_R1_001.fastq.gz out/Fig.5F_Y2384Cortex_ABE_S182_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_Y2385Ctx-GAA300_ABE_S170_L001_R1_001.fastq.gz out/Fig.5F_Y2385Ctx-GAA300_ABE_S170_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_Y2389-Ctx_ABE_S159_L001_R1_001.fastq.gz out/Fig.5F_Y2389-Ctx_ABE_S159_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_Y2392-Ctx_ABE_S133_L001_R1_001.fastq.gz out/Fig.5F_Y2392-Ctx_ABE_S133_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_Y2600-GAA800-UT_S128_L001_R1_001.fastq.gz out/Fig.5F_Y2600-GAA800-UT_S128_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_Y2604-GAA300_ABE_S59_L001_R1_001.fastq.gz out/Fig.5F_Y2604-GAA300_ABE_S59_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_Y2605-GAA300_UT_S60_L001_R1_001.fastq.gz out/Fig.5F_Y2605-GAA300_UT_S60_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_Y2605-GAA300-UT_S62_L001_R1_001.fastq.gz out/Fig.5F_Y2605-GAA300-UT_S62_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_843-300-UT_S111_L001_R1_001.fastq.gz out/Fig.5F_843-300-UT_S111_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_844-300-UT_S112_L001_R1_001.fastq.gz out/Fig.5F_844-300-UT_S112_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
python main.py Fig.5F_853-300-UT_S109_L001_R1_001.fastq.gz out/Fig.5F_853-300-UT_S109_L001_R1_001 -a GGGAGGCCTAGGAAGGTGGATCACCTGAGGTCCGGAGTTCAAGACTAACCTGGCCAACATGGTGAAACCCAGTATCTACTAAAAAATACAAAAAAAAAAAAAAAA(GAA|GRR)AATAAAGAAAAGTTAGCCGGGCGTGGTGTCGCGCGCCTGTAATCCCAGCTACTCCAGA -rc --no_trim -amas 80
